estimateParams: Estimated pulse model parameters!

In pulseTD: Identification of Transcriptional Dynamics using Pulse Models via 4su-Seq Data and RNA-Seq Data

Description

It is used to estimate pulse model parameters. Transcription rates, processing rates, and degradation correspond to different pulse model parameters, respectively. The transcription rate has 6 parameters, the processing rate has 5 parameters, and the degradation rate has 4 parameters.

Usage

estimateParams(labexon, totexon, totintr, TimeGrid, tL,
  clusterNumber = NULL, loopnumber = 50, message = TRUE)

Arguments

labexon	A matrix containing expression levels of 4su exons.For the calculation of the expression value, see estimateExpression
totexon	A matrix containing expression levels of total exons.For the calculation of the expression value, see estimateExpression
totintr	A matrix containing expression levels of total introns.For the calculation of the expression value, see estimateExpression
TimeGrid	A vector of points in time at which experimental data is collected, not allowed to be repeated
tL	4sU labeled time during the experiment
clusterNumber	Given the number of cluster cores, the default is the maximum number of available cores
loopnumber	The number of iterations of the gradient descent when solving the parameter. The default is 50.
message	Whether to print the log, the default is TRUE

Value

A 'pulseTDmodel' containing the expression values of the filtered genes, a list of solved parameters, and some basic parameter information

Examples

data('rpkmSim', package='pulseTD')
rpkm_TL <- rpkmSim$labexon[1:2,]
rpkm_PT <- rpkmSim$totintr[1:2,]
rpkm_TT <- rpkmSim$totexon[1:2,]
TimeGrid <- c(0, 15, 30, 45, 60, 75, 90, 105, 120, 135, 150, 165, 180)
tL <- 10

pulseRates<- estimateParams(rpkm_TL,rpkm_TT,rpkm_PT,TimeGrid,tL,clusterNumber=1,loopnumber=10)

pulseTD documentation built on May 17, 2019, 5:03 p.m.